In real life, Charles Darwin was a member of the Gourmet or Glutton society which involved eating, not necessarily endangered, but unusual animals such as parakeets and owls.
The inhabitants of the "plague ship" are clearly lepers, and were named as such in the trailer. The word leper was removed from the finished film after complaints by a Leprosy charity organization.
When released in the US, the film's original title was changed from 'The Pirates! In an Adventure with Scientists!' to 'The Pirates! Band of Misfits,' with some of the original voice cast replaced with American actors. The Netflix version in the UK and Ireland retain the original cast however use the US title, although the end credits do not credit any actor with their performance.
On entering Blood Island port a sign can be seen saying "twinned with Weston Super Mare" which is a seaside town close to Bristol where Aardman Animation is based.
In the scene below deck in the Pirate Captain's office, there is a list of boat rules seen on beside the door, when Number 2 walks in. It says:
Boat rules:
1. The captain is always right.
2. Players must take turns rolling the dice.
3. Don't use pigs as cannonballs.
4. Don't over accessorise.
5. Don't rain on the Pirate Captain's parade.
6. No Parades.
7. Use your inside voice below decks.
8. No whelk balancing.
9. Don't throw over empty yoghurt pots - they make excellent containers for small plants.
10. No matter how much they cry, no matter how much they beg, never feed them after midnight.